Genetic Imprinting (Megee L3)

Question 0

What is an epigenetic effect?

Answer 0

When the (heritable) expression of a gene is affected by factors other than the primary DNA sequence.
Covalent alterations such as
*cytosine methylation
*modification or substitution in chromatin of specific histone types (Thank you Dr. Ford!)

Question 1

What is genomic imprinting?

Answer 1

Differences in gene expression between the allele inherited from the mother and the allele inherited from the father.

Individual is functionally hemizygous for the gene.

Question 2

What is the epigenetic mark that mediates genetic imprinting?

Answer 2

DNA methylation

Question 3

Briefly outline the DNA methylation —> gene silencing pathway

Answer 3

1. A locus is methylated following replication
2. Selective interaction of MeCP2 with metylated DNA
3. ATP hydrolysis
4. Histone deacetylation followed by histone methylation (H3)
5. Chromatin is now compacted, histones are hypoacetylated
6. Transcription is now repressed

Question 4

What enzyme maintains the methylation of DNA after replication?

Answer 4

Maintenace Methyltransferase

At each round of replication, the newly synthesized strand of DNA is not methylated until maintenace methyltransferase comes in to selectively methylate the C in CpG’s

Question 5

Where are the CpG dinucleotides that are methylated generally found in relation to a gene?

Answer 5

Within the promoter region of an imprinted gene.

Question 6

What are two proposed mechanisms by which DNA methylation silences genes?

Answer 6

1. directly inhibiting trxn by repelling trxn factors

2. methylation actively recruits trxn repression factors

Question 7

What is a proposed mechanism by which DNA methylation acts as a gene activator?

Answer 7

may prevent binding of trxn repressors

Question 8

Imprinted genes tend to be __________ rather than __________. (location along the DNA)

Answer 8

clustered together rather than spread apart

Question 9

Imprinted genes contain maternally or paternally derived genes?

Answer 9

Both

Question 10

Do imprinted genes encode only proteins?

Answer 10

No. proteins and non-coding RNA’s

Question 11

When are epigenetic marks applied to the genome?

Answer 11

in gametes. when maternal and paternal DNA are still separate and can be modified differentially.

Question 12

Why does DNA methylation need to be reversible in genetic imprinting?

Answer 12

So that it can be reset during gametogenesis to transmit the appropriate sex-specific imprint to progeny

Question 13

What are the three “rules” that genetic imprinting follows?

Answer 13

DNA methylation marks…

1. are established in the gamete
2. are stably maintained in the somatic cells after fertilization
3. are reversible so can be reset at gametogenesis

Question 14

There are _______ major types of histones in human DNA.

________ copies of the ________ core histones (list them) make up the _________ around which DNA winds like thread around a spool.

Answer 14

5
2
4 (H2A, H2B, H3, H4)
octamer (nucleosome)

Question 15

What is the H1 histone?

Answer 15

The 5th histone that binds the DNA to the edge of the nucleosome.

Question 16

The pattern of major and specialized histone types along with their modifications is known as the _______________.

Answer 16

histone code

Question 17

Describe the distribution of imprinted genes throughout the genome.

Answer 17

Clustered together on a small subset of the autosomes rather than dispersed

Question 18

What do maintenance methyltransferase enzymes do?

Answer 18

They recognize hemi-methylated (newly synth) DNA and restores the methylation state on the new strand.

Question 19

In genetic imprinting, which gene is silenced: the methylated allele or the unmethylated allele?
Why?

Answer 19

The methylated allele is silenced. The CpG repeat region is located in the promoter region of a gene. When methylated, Methyl Cpg Binding Proteins bind and effectively block trxn machinery. So the methylated gene is OFF and the unmethylated gene is ON.

Question 20

What happens to imprinted genes in gametogenesis?

Answer 20

Methylations are erased effectively resetting the imprinting. Then, if the individual is a female, one set of “imprinted” genes are methylated (= silenced). If the individual is a male, the complimentary set of “imprinted” genes are methylated (=silenced).

Question 21

If erasure and resetting of imprinted genes does not occur during gametogenesis what would be observed in the resulting offspring?

Answer 21

Offspring could have one of the following:
1. no active copies of a gene
2. two active copies of a gene
(it could also happen by chance that the correct imprinting is carried through in some gametes)

Question 22

A deletion on which chromosome will lead to either Prader-Willi syndrome or Angleman syndrome

Answer 22

on the long arm of chromosome 15 interval q11 - a13 is deleted

del(15q11-q13)

Question 23

Del(15q11-q13) on Mom’s chromosome 15 results in what syndrome?

Answer 23

Angleman’s syndrome

Question 24

Del(15q11-q13) on Dad’s chromosome 15 results in what syndrome?

Answer 24

Prader-Willi syndrome

Question 25

On the __________ allele, the Prader-Willi gene is normally transcriptionally silenced.

Answer 25

maternal

Question 26

The expression of the Prader-Willi gene normally comes ONLY from the ________ allele.

Answer 26

paternal

Question 27

The expression of the Angleman gene normally comes ONLY from the __________ allele.

Answer 27

maternal

Question 28

Angleman syndrome is caused by defects in the expression of __________ which encodes a ______________ involved in early brain development.

Answer 28

UBE3A

ubiquitin ligase

Question 29

Prader-Willi syndrome is (currently thought to be) caused by defects in ____________ which may be involved in mRNA modification, possibly by modulating_____________.

Answer 29

SNORD116 snoRNA genes (non-coding RNA’s typically involved in guiding modifications of other RNA’s)

alternative splicing.

Question 30

What is Uniparental Disomy?

Answer 30

Both autosomes are inherited from one parent.

Question 31

What would be a likely cause of uniparental disomy?

Answer 31

1. Nondisjunction during meiosis I, resulting in a diploid gamete from parent 1.
2. Upon fertilization, zygote is now trisomic
3. If mitotic nondisjunction then results in the loss of the chromosome from parent 2, leaving only parent 1’s two copies, the conceptus now has two copies of the chromosome, but both are from parent 1.

Question 32

Nondisjunction is more likely during maternal or paternal meiosis?

Answer 32

maternal

Question 33

Whys is uniparental disomy a more common cause of Prader-Willi syndrome than of angelman syndrome?

Answer 33

Meiotic nondisjunction is more likely in the maternal gameteogenesis.

It is thus more likely that Mom contributes two transcriptionally silent PW genes. If Dad’s chromosome 15 is not present, PW syndrome results.

Question 34

What percent of PW syndrome cases are due to uniparental disomy and which parent do the two chromosome 15’s come from?

Answer 34

25%

both maternal chromosome 15’s (which are trxn’ly silent for SNORD116)

Question 35

What percent of Angelman syndrome cases are due to uniparental disomy and which parent do the two chromosome 15’s come from?

Answer 35

s (which are trxnly silenced for UBE3A)

Question 36

What percentage of the genes in the human genome are subject to genetic imprinting?

Answer 36

1%

Question 37

Histone 3, Lysine 4 (H3K4) is a(n) ____________ methylation.

Answer 37

activating

Question 38

What region on the DNA initiates the imprinting process and what do we know about the mechanism of action?

Answer 38

Imprinting centers - DNA elements located within imprinted genes are the governing elements of imprinting.

We know very little about their mechanism of action…

Question 39

What is Albright Hereditary Osteodystrophy?

Answer 39

AHO is a fully penetrant autosomal dominant trait
obesity, short stature, subcutaneous calcifications, brachydactyly (4th, 5th metacarpals)

Often, but not always, associated with PHP (pseudohypoparathyroidism)
GNAS gene is defective
*** is an example of maternal / paternal imprinting only in certain tissues

(see p. 137-139 from reading list in Megee’s L3)